gc()
## used (Mb) gc trigger (Mb) max used (Mb)
## Ncells 468544 25.1 1005840 53.8 665714 35.6
## Vcells 875351 6.7 8388608 64.0 1819492 13.9
rm(list=ls())
library(tidyverse)
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
## ✓ ggplot2 3.3.5 ✓ purrr 0.3.4
## ✓ tibble 3.1.6 ✓ dplyr 1.0.7
## ✓ tidyr 1.1.4 ✓ stringr 1.4.0
## ✓ readr 2.1.1 ✓ forcats 0.5.1
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()
library(plotly)
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
library(reticulate)
library(ade4)
library(reticulate)
library(htmltools)
library('Ternary')
setwd(dir = "/scratch/anissa.el/ImmuneStates/")
NBCELLTYPES = 17
CELLTYPES <- c('CD8-T', 'Other immune', 'DC / Mono', 'CD3-T', 'B', 'NK', 'Keratin-positive tumor', 'Tumor','CD4-T', 'Mesenchymal-like', 'Macrophages', 'Endothelial', 'Tregs', 'Unidentified', 'DC', 'Mono / Neu','Neutrophils')
MarkersCellsTMENS <- readRDS("./markers_cells_tmens.rds")
selectedMarkers <- readRDS("./selected_markers_cells.rds")
#### CD4-T
#,results = 'asis'
#CellTypes.toPlot <- unique(selectedMarkers[["cell_type"]])
library('IRdisplay')
Markers.toPlot <-selectedMarkers%>%filter(cell_type == "Tregs")%>%pull(marker)
# PlotsList <- list()
# PlotsList <- lapply(Markers.toPlot, function(marker1){
# fig <- plot_3D_ternary_cell_markers("CD4-T", marker1)
# print(htmltools::tagList(fig))
# #cat(as.character(htmltools::tagList(fig)))#,browse=TRUE
# #htmlwidgets::saveWidget(fig,"fig1.html")
# #htmltools::html_print(fig)
# })
plot_3D_ternary_cell_markers("Tregs", Markers.toPlot[1])
0% 10% 50% 80% 99%
0.84528 4.17440 9.09330 14.42200 26.45400
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
plot_3D_ternary_cell_markers("Tregs", Markers.toPlot[2])
## 0% 10% 50% 80% 99%
## -0.086878 -0.086878 -0.086878 -0.086878 18.010600
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
plot_3D_ternary_cell_markers("Tregs", Markers.toPlot[3])
## 0% 10% 50% 80% 99%
## -0.03418 -0.03418 -0.03418 -0.03418 18.25640
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels